readAll

Function

readAll

Read all sequence records from a SequenceStream object.

int readAll(ids, seqs, seqIO)

int readAll(ids, seqs, quals, seqIO)

Include Headers

seqan/seq_io.h

Parameters

ids	The identifiers of the sequence are written here. Types: StringSet of CharString.
seq	The sequence of the record is written here. Types: StringSet
quals	The qualities of the sequence is written here. Optional. Types: StringSet of CharString. Remarks: If the sequences have no qualities, as in FASTA files, the StringSet will contain empty strings.
seqIO	The SequenceStream object to read from. Types: SequenceStream

Return Values

An integer, 0 on success, 1 on errors.

Types: int

Member of

SequenceStream

Examples

Read the sequences of a FASTA file.

int main()
{
    seqan::SequenceStream seqIO("in.fasta", seqan::SequenceStream::READ_ALL);
    seqan::StringSet<seqan::CharString> ids;
    seqan::StringSet<seqan::Dna5String> seqs;

    int res = readAll(ids, seqs, seqIO);
    if (res != 0)
    {
        std::cerr << "ERROR: Could not read records!\n";
        return 1;
    }

    return 0;
}

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